Electron capture dissociation (ECD)1,2 and electron transfer dissociation (ETD)3-5 are two analytically useful techniques for obtaining polypeptide amino acid sequence information. For ECD, the electron capture cross section is predicted to be dependent on the square of the cation charge.6 A similar rate dependence upon charge has been observed for ion/ion reactions.7 A complication associated with both ECD and ETD, as currently practiced, is the possibility for sequential electron capture or electron transfer reactions. For example, first generation products can undergo sequential reactions that lead to higher generation products to the point where, in the extreme case, all cations are neutralized. Such sequential reactions are problematic because they can decrease the overall signal level of informative fragment ions and create spectral complication due to the appearance of internal fragment ions. According to some researchers8, the maximum obtainable fragmentation efficiency in ECD is 43.75% for doubly charged ions, and is not likely to exceed 50% for higher charge states while other researchers6 have reported that ECD efficiency is usually 30%. Furthermore, it has been suggested that secondary internal product ions are minimal when a significant amount of the precursor ion remains unreacted and the maximum efficiency is reached when two thirds of the precursor ions have reacted.6,9 Ideally, however, it is desirable to convert all precursor ions into structurally informative products. To this end, it is desirable to minimize contributions from second and higher generation sequential reactions while maximizing the fraction of parent ions that undergo reaction.
It has been shown that rates of selected ion/ion reactions in a quadrupole ion trap can be inhibited by applying a single frequency dipolar resonance excitation voltage to the end-caps, in a process termed “ion parking”.10 This method is effective for parking ions of a selected m/z ratio, as the resonant excitation increases the velocities of the selected ions, greatly reducing their reaction rates and also reducing the spatial overlap of oppositely charged ions. Alternatively, some have employed the use of a dipolar DC voltage across the endcaps to control charge neutralization in a quadrupole ion trap mass spectrometer.11,12 The method is effective at parking ions above a selected m/z ratio, by physically separating the cation and anion clouds on the basis of pseudopotential well-depth, which is related to m/z ratio under a fixed set of ion storage conditions.